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Genomic Loci Affecting Milk Production in German Black Pied Cattle (DSN)

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Genomic Loci Affecting Milk Production in German Black Pied Cattle (DSN) fgene-12-640039 March 2, 2021 Time: 17:46 # 1 ORIGINAL RESEARCH published: 08 March 2021 doi: 10.3389/fgene.2021.640039 Genomic Loci Affecting Milk Production in German Black Pied Cattle (DSN) Paula Korkuc´ 1, Danny Arends1, Katharina May2, Sven König2 and Gudrun A. Brockmann1* 1 Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Animal Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany, 2 Institute of Animal Breeding and Genetics, Justus-Liebig-University of Giessen, Giessen, Germany German Black Pied cattle (DSN) is an endangered population of about 2,550 dual- purpose cattle in Germany. Having a milk yield of about 2,500 kg less than the predominant dairy breed Holstein, the preservation of DSN is supported by the German government and the EU. The identification of the genomic loci affecting milk production Edited by: Ino Curik, in DSN can provide a basis for selection decisions for genetic improvement of DSN in University of Zagreb, Croatia order to increase market chances through the improvement of milk yield. A genome- Reviewed by: wide association analysis of 30 milk traits was conducted in different lactation periods Lingyang Xu, Institute of Animal Sciences, Chinese and numbers. Association using multiple linear regression models in R was performed Academy of Agricultural Sciences, on 1,490 DSN cattle genotyped with BovineSNP50 SNP-chip. 41 significant and 20 China suggestive SNPs affecting milk production traits in DSN were identified, as well as 15 Doreen Becker, Leibniz Institute for Farm Animal additional SNPs for protein content which are less reliable due to high inflation. The Biology (FBN), Germany most significant effects on milk yield in DSN were detected on chromosomes 1, 6, and *Correspondence: 20. The region on chromosome 6 was located nearby the casein gene cluster and the Gudrun A. Brockmann [email protected] corresponding haplotype overlapped the CSN3 gene (casein kappa). Associations for fat and protein yield and content were also detected. High correlation between traits of Specialty section: the same lactation period or number led to some SNPs being significant for multiple This article was submitted to Livestock Genomics, investigated traits. Half of all identified SNPs have been reported in other studies, a section of the journal previously. 15 SNPs were associated with the same traits in other breeds. The other Frontiers in Genetics associated SNPs have been reported previously for traits such as exterior, health, meat Received: 10 December 2020 Accepted: 11 February 2021 and carcass, production, and reproduction traits. No association could be detected Published: 08 March 2021 between DGAT1 and other known milk genes with milk production traits despite the Citation: close relationship between DSN and Holstein. The results of this study confirmed that Korkuc´ P, Arends D, May K, many SNPs identified in other breeds as associated with milk traits also affect milk traits König S and Brockmann GA (2021) Genomic Loci Affecting Milk in dual-purpose DSN cattle and can be used for further genetic analysis to identify genes Production in German Black Pied and causal variants that affect milk production in DSN cattle. Cattle (DSN). Front. Genet. 12:640039. Keywords: genome-wide association study, cattle, SNP chip, Holstein cattle, CSN3 gene, DGAT1 gene, casein doi: 10.3389/fgene.2021.640039 gene Frontiers in Genetics| www.frontiersin.org 1 March 2021| Volume 12| Article 640039 fgene-12-640039 March 2, 2021 Time: 17:46 # 2 Korkuc´ et al. GWAS for Milk Traits in DSN INTRODUCTION MATERIALS AND METHODS German Black Pied cattle (DSN, “Deutsches Schwarzbuntes Populations Niederungsrind”) is an endangered breed of about 2,550 dual- Data of 1,816 DSN cows was available for this study. These cows purpose cattle in Germany. The ancestor population of this represent about two thirds of the DSN population registered breed is considered as one of the founder populations of in Germany (The Society for the Conservation of Old and the nowadays dominantly used high yielding German Holstein Endangered Livestock Breeds (GEH), 2018). The cows were born breed (Köppe-Forsthoff, 1967; Grothe, 1993), which is one between 2005 and 2016, and descended from 76 sires. Cows reason why the German government and the European Union were raised on six farms. In order to reduce environmental support its preservation. This support is necessary because influences, we filtered to have at least 20 DSN cows per farm, milk yield of DSN cows is about 2,500 kg less compared to per sire, and per birth year. This reduced the data set to 1,490 German Holstein, which has led to the replacement of DSN DSN cows from five farms, born between 2007 and 2016, and by Holstein cattle. Although DSN is a dual-purpose breed, descending from 28 sires. milk yield is the main contributor to the economic merit In order to compare the results that we obtained in DSN with and meat yield and carcass quality do not compensate the German Holstein, we used GWAS results previously obtained lower milk yield. in our lab on a population of 2,400 German Holstein bulls. The interest in preservation of DSN does not only stem This population has been used and described in detail repeatedly from its relationship to Holstein cattle and retaining genetic (Zielke et al., 2011, 2013; Abdel-Shafy et al., 2018). diversity as a gene reserve for the future. The interest in DSN cattle is also due to their advantageous traits. For Phenotypes example, the milk fat and protein content with 4.3 % and Milk traits with corresponding pedigree data were obtained 3.7 %, respectively, is higher compared to German Holstein from the cattle breeding association “RBB Rinderproduktion (RBB Rinderproduktion Berlin-Brandenburg GmbH., 2020). Berlin-Brandenburg GmbH” in April 2020. Traits included Moreover, DSN cattle are considered to be more robust for milk, fat, and protein yield in kilogram (milk kg, fat kg, and grazing and more fertile. protein kg) for three lactation periods: 100-days (100d), 200- One of the long-term goals for maintaining DSN is to days (200d), and 305-days (305d). 305 days data was available reduce governmental financial support by increasing economic for the first three lactations (LA1, LA2, and LA3), whereas value of the breed through the improvement of milk yield. 100 and 200 days data was available only for LA1. 305 days Simultaneously, the advantageous traits and the typical body data of cows with < 270 days in milk was not considered. composition of this dual-purpose breed should be maintained. Fat and protein content (fat %, protein %) were calculated by So far, little is known about the genes affecting milk traits dividing fat or protein kg by milk kg of the respective lactation. in DSN. Recently, genome-wide association studies (GWAS) The lactation mean (LAm) was calculated for cows with full in DSN for health traits identified three significant and two data in the first three lactations. This leads to a total of 30 suggestive SNPs for clinical mastitis (Meier et al., 2020) and investigated milk traits in this study. For each trait, outliers 44 significant SNPs for endoparasite resistance (May et al., were defined as values outside the 1.5 times interquartile range 2019). Another study, investigating genomic variation in the within each farm and removed from the data set. This leads casein gene cluster, found three protein variants of CSN2 and to data being available for 1,478, 1,476, 1,372, 1,160, 862, and CSN3 and fixed protein variants for CSN1S1 and CSN1S2 685 DSN cows in LA1 (100d), LA1 (200d), LA1, LA2, LA3, and (Meier et al., 2019). In contrast, 63,404 associations with LAm, respectively. milk traits in general were available from Cattle QTLdb Release 42 (accessed 09/21/2020) (Hu et al., 2019), whereof Genotypes around 79 % were found in studies with Holstein cattle. DSN cattle cows were genotyped using the Illumina R Furthermore, 10 % of the reported associations in those Bovine50SNP v3 BeadChip (Illumina, Inc., 5200 Illumina studies with Holstein cattle are reported within the first Way, San Diego, CA, United States). SNP chip probe sequences 10 Mb on chromosome 14, where the DGAT1 gene is located were remapped against the Bos taurus genome version ARS- which is known to influence milk yield and composition UCD1.2 (Rosen et al., 2018) using NCBI Nucleotide-Nucleotide (Grisart et al., 2002). BLAST version 2.2.31C (Altschul et al., 1990) in order to obtain In this study, we investigated the genetic basis contributing to genome positions for SNPs on the ARS-UCD1.2 genome build. the variation in milk performance of the current DSN population SNP probes that mapped to multiple genomic locations were by GWAS. Since the DSN population is small, power to find removed. Genotype quality control was performed for animals significant genomic loci is limited. Nevertheless, there is an and SNPs. SNP calls with a GC-score < 0.7 were set to missing. urgent need to provide genetic association information for small Animals with a call rate < 90% were discarded. SNPs with a endangered populations to support their preservation and further call rate < 95% and a minor allele frequency (MAF) < 5% were development. Even if not all genomic loci are significantly removed. Lastly, genotype groups with less than 30 observations detectable, the obtained results in DSN and the comparison were set to missing to prevent spurious association. After to related breeds provide a basis for selection decisions to quality control, 36,929 high confident SNPs were available for genetically improve DSN. further analysis. Frontiers in Genetics| www.frontiersin.org 2 March 2021| Volume 12| Article 640039 fgene-12-640039 March 2, 2021 Time: 17:46 # 3 Korkuc´ et al. GWAS for Milk Traits in DSN Genome-Wide Association Study null model TYs D .1janimals)] and the null model extended Genome-wide association studies was performed with multiple with one of the covariates [Yxs D covariatex C .1janimals/] linear regression models implemented in the R language for (Supplementary Table 3).
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